Hi Anastasia,
An independent T-test on the aseg.stats WM-Hypointensties (SegId 77) showed
that the mean WM hypointensities volume of the patient group (1378.8mm3, SD
650mm3) did not significantly differ from the controls (1120.8mm3, SD 372mm3;
p=.111). A Pearson and Spearman correlation
Hello Sir/Madam,
I am currently running a statistical test using the FSGD method. I am
encountering a problem in relation to the creation of the glmdir folder
when I run the mri_glmfit function. I recieve an ERROR message that tells
me that the design matrix (automatically generated) is ill
Hi Anupa
it's pretty hard to figure anything out from your images. What is wrong
with using the cutting plane tool? You specify 3 points to define the
plane, then a 4th to specify which side you want to keep
cheers
Bruce
On Wed, 3 Apr 2013,
Anupa AV wrote:
- Forwarded Message -
this is for the same acquisition? You should definitely try to avoid that
as it will change the SNR.
Bruce
On Wed, 3 Apr 2013, Anupa AV wrote:
Dear All,
I use Philips Achieva 3T scanner for the MRI study.
When I open the Dicom folder, (say for MPR ) the no. of items I can see is
222
Hi list,
I'm reading a lot of post on this list about cortical thickness normalization.
I' m noting very different results on my data when I use mean thickness or ICV
as nuisance factor than no factor.
I'm confuse on this topic, could you advise the best way, please?
Thanks,
Stefano
If you're studying thickness, I'm a fan of using mean cortical thickness as
the covariate (since thickness is what you're studying). I've posted on
this in the past.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the
Dear Freesurfer experts,I'm having troubles when setting a permutation test, I'm making group comparisons, but I'm introducing the Age, and cortical thickness as niusance variables (as previously recommended).It seems that permutations only work for orthogonal matrices, does this means that I
Thank you very much, Michael!
I have just an other important question, please.
I'm performing cortical thickness analysis on three groups. One of this is a
control group and I'm using it as support because I'm interested only to
difference between the two groups of disease.
These are my
Hello All,
I am trying to use mri_robust_register to compute the symmetric rigid
registration for inverse consistency. Is there a way to output the inverse
consistent jacobian for the same registration?
Thank you,
Jay
___
Freesurfer mailing list
Hi,
i read the following in a paper and would like to do the same:
At each vertex in each hemisphere, the proportion of total variance in
cortical thickness (CT) accounted for by 2 linear regression models was
compared: One that did not include an age-by-group interaction term, Model
1: [CT =
Hi Jay
for the rigid case the jacobian is always the same.
cheers
Bruce
On Thu, 4 Apr 2013,
Jayachandra Raghava wrote:
Hello All,
I am trying to use mri_robust_register to compute the symmetric rigid
registration for inverse
consistency. Is there a way to output the inverse consistent
Hi, I can confirm the problem with Fedora 18 is that former glibc version
would accept unsupported salt values, but newer versions
of the library have become stricter. More details at
https://bugzilla.redhat.com/show_bug.cgi?id=905638
I can also say you can run tkmedit, tksurfer and freeview if
Hi Joshua, you should start by not coding gender and handedness as
continuous variables. In doing this, you are saying that you expect
right handers to have 2x the thickness as left handers (or females to
have 2x the thickness as males). You need 8 classes. If your voxel
variable is discrete,
Correct, you cannot do a permutation test with continuous variables (or
with any non-orthogonal design matrix). If you use the --perm-force, it
will do the permutation test as normal (by randomly swapping the rows),
but technically the test is not legal. Having said that, I suspect that
LOTS
What do you want to do exactly? Test whether adding the age*group
interaction is significant? If so, then you can just run model2 with a
contrast looking at that term (or those terms). BTW, it would seem that
the model they describe would be ill-conditioned because age*b2 and
group*age*b3
Hi,
Sorry, but I don't understand what you're asking.
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Yes,
I meant that the output labels were much less than the input ones and I
would not expect this, but their position was correct.
I will try to figure out if I did something wrong.
Thank you!
Eleonora
2013/4/4 Douglas Greve gr...@nmr.mgh.harvard.edu
When you say it does not work, what do
An alternative approach would be to use bootstrapping to determine the
significance as was done by Gross et al. 2012. *Cortical signatures of
cognition and their relationship to Alzheimer's disease.*
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of
Hi Doug,
There are approaches/methods available for permutation testing with
non-orthogonal design matrices -- see for example the documentation for
FSL's randomise and the references cited therein.
cheers,
-MH
--
Michael Harms, Ph.D.
Yes, I know, I just have not implemented them:).
doug
On 04/04/2013 12:47 PM, Michael Harms wrote:
Hi Doug,
There are approaches/methods available for permutation testing with
non-orthogonal design matrices -- see for example the documentation for
FSL's randomise and the references cited
I'm sorry.
I'm performing the cortical thickness analysis on three groups (2 pathological
groups and 1 control group).
I'm interested mainly to the differences between the two groups of disease.
These are my questions:
1- Is qdec a good option for my study design or I should use other glm option
1) If you are ONLY interested in the difference between the 2 pathological
groups, then you can include just those two. If you are also interested in
comparing either of those with control, then I'd personally opt for a single
model that includes all 3 groups, in which you investigate the
I noticed it was taking 6-7 seconds to read in a wfile (scalar surface
overlay) into matlab using fast_read_wfile.m. In case anybody else finds
this annoying, here's a faster alternative that produces identical output:
in fast_read_wfile.m, replace everything after the first fread line with:
Dear Freesurfer experts,
After I ran the functional to structural registration using the bbregister
command, it looks like the dorsal part of the brain for this participant
is cut off in the BOLD images. When we ran the scan, we made sure that the
slice prescription covered the entire brain. We
Did you compare the number of slices to that of your sequence? I have had
issues when overzealously pulling data off of bourget (that is before the
files have completed being sent). A simple re-conversion to mgz (or
whatever format you prefer) has fixed this when waiting a bit longer till
bourget
Hm, it doesn't sound like a failure in the tract reconstruction then. What
areas does TBSS give you differences in? Is it in the area of the same
tracts?
On Thu, 4 Apr 2013, Sean Hatton wrote:
Hi Anastasia,
An independent T-test on the aseg.stats WM-Hypointensties (SegId 77) showed
that
Dear Bruce,
Thank you for your response. I just looked at the f.nii file using fslview
and it looks like the top is cut off.
Trang
what are you visualizing it in? If you just look at it without the
registration does it look ok?
On Thu, 4 Apr 2013,
qtngu...@nmr.mgh.harvard.edu wrote:
Dear
The increase in FA in patients is strange indeed. Are there any outliers
in the tract averages? (Sorry if you've already mentioned this.)
There are definitely situations in which TBSS and tracula would give you
different results, since tracula gives you average FA in a large bundle,
whereas
There are no extreme outliers (only 3 moderate outliers). Regarding the
position, is that the FA center measures?
Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote:
The increase in FA in patients is strange indeed. Are there any outliers
in the tract averages? (Sorry if you've already
It's the pathstats.byvoxel.txt file.
On Thu, 4 Apr 2013, Sean Hatton wrote:
There are no extreme outliers (only 3 moderate outliers). Regarding the position, is that
the FA center measures?
Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote:
The increase in FA in patients is strange
$ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login
Logging in to :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:2401/usr/fscvsroot
CVS password: [hidden]
cvs [login aborted]: connect to fsvm.nmr.mgh.harvard.edu(155.52.242.23):2401
failed: Connection timed out
Is this a known
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